Assuming you are not using a build tool like Maven*: You manipulate the build path by editing the build path in the project properties. You can select what to export there too. If you want to manipulate the runtime configurations you would edit it in menu "Run", "Runtime configurations...".
* and even if, but then it is not persistent
I’ve looked at a lot of different solutions, and in my humble opinion Aspose is the way to go. Here’s the link: http://aspose.com